Starting phenix.real_space_refine on Sun Mar 10 22:49:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gb3_29912/03_2024/8gb3_29912.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 242 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 3420 2.51 5 N 996 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5537 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3814 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1051 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 672 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 3.30, per 1000 atoms: 0.60 Number of scatterers: 5537 At special positions: 0 Unit cell: (68.724, 86.112, 106.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1113 8.00 N 996 7.00 C 3420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 46.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'D' and resid 51 through 61 removed outlier: 4.390A pdb=" N GLN D 57 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 4.289A pdb=" N SER D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 200 through 220 removed outlier: 3.640A pdb=" N TRP D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 274 through 288 removed outlier: 6.054A pdb=" N ASP D 284 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 300 removed outlier: 4.251A pdb=" N THR D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.521A pdb=" N THR D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.508A pdb=" N LYS D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 496 removed outlier: 3.736A pdb=" N ASP D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 488 " --> pdb=" O GLU D 484 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 491 " --> pdb=" O ASP D 487 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 removed outlier: 3.760A pdb=" N GLU D 505 " --> pdb=" O ARG D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'E' and resid 45 through 79 removed outlier: 3.592A pdb=" N GLN E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.866A pdb=" N ALA E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.950A pdb=" N GLY E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 83 removed outlier: 3.773A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.677A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 107 removed outlier: 4.117A pdb=" N GLY F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 117 through 130 removed outlier: 4.119A pdb=" N ASP F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.769A pdb=" N VAL D 16 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA D 4 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 177 through 181 Processing sheet with id=AA3, first strand: chain 'D' and resid 381 through 386 removed outlier: 3.747A pdb=" N LEU D 385 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU D 373 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN D 413 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY D 429 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN D 416 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU D 427 " --> pdb=" O GLN D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 169 removed outlier: 3.577A pdb=" N VAL E 163 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY E 185 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL E 167 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU E 183 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 172 through 174 removed outlier: 7.796A pdb=" N TYR E 172 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 179 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 174 " --> pdb=" O GLN E 177 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 768 1.46 - 1.57: 2847 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 5597 Sorted by residual: bond pdb=" CA ILE D 39 " pdb=" CB ILE D 39 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.39e+00 bond pdb=" CG PRO D 393 " pdb=" CD PRO D 393 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.47e-01 bond pdb=" CB PRO D 148 " pdb=" CG PRO D 148 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 6.93e-01 bond pdb=" CB VAL D 345 " pdb=" CG1 VAL D 345 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.44e-01 bond pdb=" C LYS D 361 " pdb=" O LYS D 361 " ideal model delta sigma weight residual 1.242 1.234 0.008 1.00e-02 1.00e+04 6.26e-01 ... (remaining 5592 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 140 107.21 - 113.90: 3268 113.90 - 120.60: 2166 120.60 - 127.29: 1957 127.29 - 133.99: 38 Bond angle restraints: 7569 Sorted by residual: angle pdb=" C LYS D 361 " pdb=" CA LYS D 361 " pdb=" CB LYS D 361 " ideal model delta sigma weight residual 116.63 110.78 5.85 1.16e+00 7.43e-01 2.54e+01 angle pdb=" C THR D 391 " pdb=" N ILE D 392 " pdb=" CA ILE D 392 " ideal model delta sigma weight residual 120.43 124.79 -4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" C ILE D 144 " pdb=" N VAL D 145 " pdb=" CA VAL D 145 " ideal model delta sigma weight residual 120.49 125.08 -4.59 1.38e+00 5.25e-01 1.10e+01 angle pdb=" CA LYS D 361 " pdb=" C LYS D 361 " pdb=" N ASP D 362 " ideal model delta sigma weight residual 119.63 117.09 2.54 8.10e-01 1.52e+00 9.84e+00 angle pdb=" C ILE D 392 " pdb=" CA ILE D 392 " pdb=" CB ILE D 392 " ideal model delta sigma weight residual 113.70 110.84 2.86 9.50e-01 1.11e+00 9.03e+00 ... (remaining 7564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 3139 15.77 - 31.55: 214 31.55 - 47.32: 59 47.32 - 63.10: 14 63.10 - 78.87: 6 Dihedral angle restraints: 3432 sinusoidal: 1348 harmonic: 2084 Sorted by residual: dihedral pdb=" CA ALA D 105 " pdb=" C ALA D 105 " pdb=" N TYR D 106 " pdb=" CA TYR D 106 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU D 366 " pdb=" C LEU D 366 " pdb=" N ASP D 367 " pdb=" CA ASP D 367 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN D 45 " pdb=" C ASN D 45 " pdb=" N GLY D 46 " pdb=" CA GLY D 46 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.051: 219 0.051 - 0.076: 96 0.076 - 0.102: 43 0.102 - 0.127: 33 Chirality restraints: 889 Sorted by residual: chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE D 253 " pdb=" N ILE D 253 " pdb=" C ILE D 253 " pdb=" CB ILE D 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CB ILE D 443 " pdb=" CA ILE D 443 " pdb=" CG1 ILE D 443 " pdb=" CG2 ILE D 443 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 886 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 291 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO D 292 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 292 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 292 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 118 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO D 119 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 52 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO D 53 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 53 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 53 " 0.018 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1115 2.78 - 3.31: 5743 3.31 - 3.84: 9218 3.84 - 4.37: 10395 4.37 - 4.90: 17457 Nonbonded interactions: 43928 Sorted by model distance: nonbonded pdb=" O ILE D 307 " pdb=" NZ LYS D 333 " model vdw 2.245 2.520 nonbonded pdb=" O PHE D 278 " pdb=" OG1 THR D 282 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP D 464 " pdb=" OG1 THR D 467 " model vdw 2.249 2.440 nonbonded pdb=" O PRO E 115 " pdb=" OG SER E 118 " model vdw 2.268 2.440 nonbonded pdb=" N GLU E 148 " pdb=" O ALA E 182 " model vdw 2.299 2.520 ... (remaining 43923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 6.740 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5597 Z= 0.194 Angle : 0.522 5.846 7569 Z= 0.305 Chirality : 0.041 0.127 889 Planarity : 0.004 0.038 1008 Dihedral : 12.387 78.869 2086 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.31 % Allowed : 8.97 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.33), residues: 723 helix: 1.00 (0.31), residues: 309 sheet: -0.68 (0.55), residues: 101 loop : -1.39 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 211 HIS 0.001 0.000 HIS E 147 PHE 0.011 0.001 PHE D 176 TYR 0.006 0.001 TYR D 106 ARG 0.003 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6699 (m-40) cc_final: 0.6446 (m-40) REVERT: D 100 LYS cc_start: 0.7758 (tttm) cc_final: 0.7533 (tttm) REVERT: D 166 ILE cc_start: 0.7430 (tp) cc_final: 0.7220 (tp) REVERT: D 227 ASP cc_start: 0.6805 (m-30) cc_final: 0.6598 (m-30) REVERT: D 229 MET cc_start: 0.5748 (tpt) cc_final: 0.5399 (tpt) REVERT: D 283 GLN cc_start: 0.6353 (tp-100) cc_final: 0.5803 (tp-100) REVERT: D 333 LYS cc_start: 0.7242 (ttmt) cc_final: 0.6792 (ttmt) REVERT: D 356 LEU cc_start: 0.7988 (mm) cc_final: 0.7552 (mm) REVERT: D 357 LYS cc_start: 0.8056 (pttm) cc_final: 0.7728 (pttm) REVERT: D 359 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6442 (mm-30) REVERT: D 383 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (p) REVERT: D 395 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7304 (tmtt) REVERT: D 416 GLN cc_start: 0.7787 (pm20) cc_final: 0.7439 (pm20) REVERT: D 489 MET cc_start: 0.6065 (mpp) cc_final: 0.5466 (mpp) REVERT: E 63 GLN cc_start: 0.6875 (pm20) cc_final: 0.6522 (pm20) REVERT: F 69 PHE cc_start: 0.7108 (t80) cc_final: 0.6471 (t80) REVERT: F 117 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7079 (ttmm) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.2177 time to fit residues: 36.5930 Evaluate side-chains 116 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN E 80 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 5597 Z= 0.442 Angle : 0.688 10.018 7569 Z= 0.365 Chirality : 0.047 0.180 889 Planarity : 0.005 0.046 1008 Dihedral : 7.793 57.662 809 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.02 % Favored : 91.84 % Rotamer: Outliers : 5.34 % Allowed : 13.62 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.32), residues: 723 helix: 0.41 (0.29), residues: 315 sheet: -0.66 (0.55), residues: 102 loop : -1.65 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 204 HIS 0.006 0.001 HIS D 72 PHE 0.022 0.002 PHE D 176 TYR 0.013 0.002 TYR D 155 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6770 (m-40) cc_final: 0.6424 (m-40) REVERT: D 49 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7035 (mp) REVERT: D 100 LYS cc_start: 0.7721 (tttm) cc_final: 0.7519 (tttm) REVERT: D 166 ILE cc_start: 0.7588 (tp) cc_final: 0.7374 (tp) REVERT: D 182 GLU cc_start: 0.4692 (mt-10) cc_final: 0.3668 (mt-10) REVERT: D 215 LYS cc_start: 0.6813 (tptp) cc_final: 0.6501 (tptp) REVERT: D 229 MET cc_start: 0.6109 (tpt) cc_final: 0.5783 (tpt) REVERT: D 283 GLN cc_start: 0.6377 (tp-100) cc_final: 0.5845 (tp-100) REVERT: D 333 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6939 (ttmt) REVERT: D 356 LEU cc_start: 0.8055 (mm) cc_final: 0.7630 (mm) REVERT: D 359 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6573 (mm-30) REVERT: D 395 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7415 (tmtt) REVERT: E 63 GLN cc_start: 0.6803 (pm20) cc_final: 0.6522 (pm20) REVERT: F 69 PHE cc_start: 0.7223 (t80) cc_final: 0.6426 (t80) REVERT: F 75 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.7069 (ttp-110) REVERT: F 78 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6400 (mmm160) REVERT: F 102 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5742 (pp) REVERT: F 117 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7105 (tppp) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.2321 time to fit residues: 36.6091 Evaluate side-chains 129 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.0170 chunk 20 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5597 Z= 0.223 Angle : 0.579 9.006 7569 Z= 0.302 Chirality : 0.043 0.143 889 Planarity : 0.004 0.043 1008 Dihedral : 7.260 59.386 805 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.66 % Allowed : 15.34 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.32), residues: 723 helix: 0.84 (0.29), residues: 309 sheet: -0.58 (0.58), residues: 92 loop : -1.61 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.017 0.001 PHE D 122 TYR 0.007 0.001 TYR D 155 ARG 0.005 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6651 (m-40) cc_final: 0.6313 (m-40) REVERT: D 56 ASN cc_start: 0.6248 (p0) cc_final: 0.5941 (p0) REVERT: D 100 LYS cc_start: 0.7759 (tttm) cc_final: 0.7533 (tttm) REVERT: D 229 MET cc_start: 0.5874 (tpt) cc_final: 0.5598 (tpt) REVERT: D 249 GLN cc_start: 0.7671 (pp30) cc_final: 0.7442 (pp30) REVERT: D 283 GLN cc_start: 0.6303 (tp-100) cc_final: 0.5754 (tp-100) REVERT: D 333 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7124 (ttmt) REVERT: D 356 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7558 (mm) REVERT: D 359 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6565 (mm-30) REVERT: D 395 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7369 (tmtt) REVERT: E 63 GLN cc_start: 0.6825 (pm20) cc_final: 0.6509 (pm20) REVERT: F 69 PHE cc_start: 0.7158 (t80) cc_final: 0.6426 (t80) REVERT: F 78 ARG cc_start: 0.6920 (mmm160) cc_final: 0.6335 (mmm160) REVERT: F 117 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7131 (ttmm) outliers start: 27 outliers final: 17 residues processed: 122 average time/residue: 0.2308 time to fit residues: 34.7422 Evaluate side-chains 123 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 chunk 34 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5597 Z= 0.239 Angle : 0.583 8.887 7569 Z= 0.306 Chirality : 0.044 0.134 889 Planarity : 0.004 0.037 1008 Dihedral : 6.987 59.890 804 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 6.03 % Allowed : 15.34 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.32), residues: 723 helix: 0.98 (0.29), residues: 309 sheet: -0.60 (0.58), residues: 92 loop : -1.62 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.015 0.001 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.006 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6707 (m-40) cc_final: 0.6359 (m-40) REVERT: D 100 LYS cc_start: 0.7758 (tttm) cc_final: 0.7518 (tttm) REVERT: D 215 LYS cc_start: 0.6727 (tptp) cc_final: 0.6432 (tptp) REVERT: D 229 MET cc_start: 0.5861 (tpt) cc_final: 0.5591 (tpt) REVERT: D 272 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: D 283 GLN cc_start: 0.6272 (tp-100) cc_final: 0.5771 (tp-100) REVERT: D 333 LYS cc_start: 0.7459 (ttmt) cc_final: 0.7195 (ttmt) REVERT: D 356 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7575 (mm) REVERT: D 359 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6569 (mm-30) REVERT: D 395 LYS cc_start: 0.7723 (tmtt) cc_final: 0.7379 (tmtt) REVERT: D 416 GLN cc_start: 0.8208 (pm20) cc_final: 0.7923 (pm20) REVERT: E 63 GLN cc_start: 0.6842 (pm20) cc_final: 0.6553 (pm20) REVERT: F 69 PHE cc_start: 0.7148 (t80) cc_final: 0.6373 (t80) REVERT: F 78 ARG cc_start: 0.6920 (mmm160) cc_final: 0.6234 (mmm160) REVERT: F 102 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5777 (pp) REVERT: F 117 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7209 (ttmm) outliers start: 35 outliers final: 20 residues processed: 125 average time/residue: 0.2349 time to fit residues: 35.9414 Evaluate side-chains 127 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5597 Z= 0.265 Angle : 0.604 11.263 7569 Z= 0.317 Chirality : 0.044 0.185 889 Planarity : 0.006 0.126 1008 Dihedral : 7.077 59.804 804 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.86 % Allowed : 16.21 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.32), residues: 723 helix: 1.00 (0.30), residues: 309 sheet: -0.66 (0.58), residues: 92 loop : -1.66 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.015 0.001 PHE D 122 TYR 0.011 0.001 TYR D 155 ARG 0.010 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6709 (m-40) cc_final: 0.6354 (m-40) REVERT: D 100 LYS cc_start: 0.7761 (tttm) cc_final: 0.7517 (tttm) REVERT: D 229 MET cc_start: 0.5826 (tpt) cc_final: 0.5541 (tpt) REVERT: D 231 MET cc_start: 0.5351 (mmt) cc_final: 0.5144 (mmt) REVERT: D 249 GLN cc_start: 0.7663 (pp30) cc_final: 0.7192 (pp30) REVERT: D 272 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: D 283 GLN cc_start: 0.6314 (tp-100) cc_final: 0.5824 (tp-100) REVERT: D 333 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7203 (ttmt) REVERT: D 356 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7581 (mm) REVERT: D 359 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6586 (mm-30) REVERT: D 395 LYS cc_start: 0.7726 (tmtt) cc_final: 0.7377 (tmtt) REVERT: E 63 GLN cc_start: 0.6827 (pm20) cc_final: 0.6576 (pm20) REVERT: F 69 PHE cc_start: 0.7171 (t80) cc_final: 0.6371 (t80) REVERT: F 102 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5795 (pp) REVERT: F 117 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7233 (ttmm) outliers start: 34 outliers final: 22 residues processed: 125 average time/residue: 0.2301 time to fit residues: 35.4124 Evaluate side-chains 131 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5597 Z= 0.229 Angle : 0.580 11.306 7569 Z= 0.302 Chirality : 0.044 0.182 889 Planarity : 0.004 0.043 1008 Dihedral : 6.829 59.658 802 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.34 % Allowed : 17.59 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.32), residues: 723 helix: 1.14 (0.30), residues: 309 sheet: -0.61 (0.58), residues: 92 loop : -1.65 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.016 0.001 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.008 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 ASN cc_start: 0.6654 (m-40) cc_final: 0.6282 (m-40) REVERT: D 100 LYS cc_start: 0.7766 (tttm) cc_final: 0.7501 (tttm) REVERT: D 229 MET cc_start: 0.5813 (tpt) cc_final: 0.5538 (tpt) REVERT: D 249 GLN cc_start: 0.7705 (pp30) cc_final: 0.7205 (pp30) REVERT: D 272 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6462 (pp30) REVERT: D 283 GLN cc_start: 0.6329 (tp-100) cc_final: 0.5769 (tp-100) REVERT: D 333 LYS cc_start: 0.7465 (ttmt) cc_final: 0.7222 (ttmt) REVERT: D 356 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7573 (mm) REVERT: D 359 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6601 (mm-30) REVERT: D 395 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7254 (tmtt) REVERT: E 63 GLN cc_start: 0.6818 (pm20) cc_final: 0.6616 (pm20) REVERT: F 69 PHE cc_start: 0.7171 (t80) cc_final: 0.6357 (t80) REVERT: F 102 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5799 (pp) REVERT: F 117 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7312 (ttmm) outliers start: 31 outliers final: 24 residues processed: 124 average time/residue: 0.2397 time to fit residues: 36.2618 Evaluate side-chains 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5597 Z= 0.220 Angle : 0.584 11.487 7569 Z= 0.304 Chirality : 0.043 0.165 889 Planarity : 0.004 0.038 1008 Dihedral : 6.747 59.431 802 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.86 % Allowed : 17.93 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.32), residues: 723 helix: 1.23 (0.30), residues: 309 sheet: -0.57 (0.58), residues: 92 loop : -1.64 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.016 0.001 PHE D 122 TYR 0.008 0.001 TYR D 155 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: D 100 LYS cc_start: 0.7779 (tttm) cc_final: 0.7513 (tttm) REVERT: D 182 GLU cc_start: 0.3870 (mm-30) cc_final: 0.3067 (mm-30) REVERT: D 229 MET cc_start: 0.5674 (tpt) cc_final: 0.5378 (tpt) REVERT: D 249 GLN cc_start: 0.7685 (pp30) cc_final: 0.7146 (pp30) REVERT: D 272 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6454 (pp30) REVERT: D 283 GLN cc_start: 0.6241 (tp-100) cc_final: 0.5769 (tp-100) REVERT: D 333 LYS cc_start: 0.7436 (ttmt) cc_final: 0.7206 (ttmt) REVERT: D 356 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 359 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6606 (mm-30) REVERT: D 384 ARG cc_start: 0.6964 (tpp80) cc_final: 0.6731 (tpp80) REVERT: D 395 LYS cc_start: 0.7633 (tmtt) cc_final: 0.7344 (tmtt) REVERT: D 396 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6748 (tpt170) REVERT: D 418 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: E 95 LEU cc_start: 0.8423 (mt) cc_final: 0.8174 (mp) REVERT: F 64 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6847 (mmt-90) REVERT: F 69 PHE cc_start: 0.7183 (t80) cc_final: 0.6402 (t80) REVERT: F 102 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5780 (pp) REVERT: F 117 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7322 (ttmm) outliers start: 34 outliers final: 20 residues processed: 126 average time/residue: 0.2399 time to fit residues: 36.8973 Evaluate side-chains 131 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5597 Z= 0.228 Angle : 0.592 11.569 7569 Z= 0.309 Chirality : 0.044 0.154 889 Planarity : 0.004 0.038 1008 Dihedral : 6.752 59.738 802 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.52 % Allowed : 18.45 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.32), residues: 723 helix: 1.20 (0.29), residues: 310 sheet: -0.55 (0.58), residues: 92 loop : -1.68 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.017 0.001 PHE D 122 TYR 0.009 0.001 TYR D 155 ARG 0.009 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: D 100 LYS cc_start: 0.7776 (tttm) cc_final: 0.7503 (tttm) REVERT: D 229 MET cc_start: 0.5686 (tpt) cc_final: 0.5394 (tpt) REVERT: D 249 GLN cc_start: 0.7705 (pp30) cc_final: 0.7167 (pp30) REVERT: D 272 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6465 (pp30) REVERT: D 283 GLN cc_start: 0.6264 (tp-100) cc_final: 0.5803 (tp-100) REVERT: D 333 LYS cc_start: 0.7430 (ttmt) cc_final: 0.7223 (ttmt) REVERT: D 356 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7532 (mm) REVERT: D 359 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6584 (mm-30) REVERT: D 384 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6731 (tpp80) REVERT: D 395 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7412 (tmtt) REVERT: D 396 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6803 (tpt170) REVERT: D 418 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: F 69 PHE cc_start: 0.7204 (t80) cc_final: 0.6456 (t80) REVERT: F 102 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5765 (pp) REVERT: F 117 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7325 (ttmm) REVERT: F 122 LYS cc_start: 0.8019 (tptt) cc_final: 0.7610 (tptt) outliers start: 32 outliers final: 21 residues processed: 124 average time/residue: 0.2481 time to fit residues: 37.3400 Evaluate side-chains 128 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 425 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5597 Z= 0.261 Angle : 0.614 11.685 7569 Z= 0.320 Chirality : 0.044 0.210 889 Planarity : 0.004 0.045 1008 Dihedral : 6.872 59.183 802 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.34 % Allowed : 18.79 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.32), residues: 723 helix: 1.15 (0.29), residues: 310 sheet: -0.59 (0.58), residues: 92 loop : -1.72 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.018 0.001 PHE D 122 TYR 0.010 0.001 TYR D 155 ARG 0.018 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 49 LEU cc_start: 0.7176 (mp) cc_final: 0.6975 (mp) REVERT: D 100 LYS cc_start: 0.7774 (tttm) cc_final: 0.7514 (tttm) REVERT: D 229 MET cc_start: 0.5753 (tpt) cc_final: 0.5476 (tpt) REVERT: D 249 GLN cc_start: 0.7739 (pp30) cc_final: 0.7228 (pp30) REVERT: D 272 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: D 283 GLN cc_start: 0.6292 (tp-100) cc_final: 0.5844 (tp-100) REVERT: D 333 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7174 (ttmt) REVERT: D 356 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7547 (mm) REVERT: D 359 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6613 (mm-30) REVERT: D 382 MET cc_start: 0.6566 (ttp) cc_final: 0.6336 (ttp) REVERT: D 395 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7405 (tmtt) REVERT: D 418 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6861 (mm-30) REVERT: F 102 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5791 (pp) REVERT: F 117 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7355 (tppp) outliers start: 31 outliers final: 23 residues processed: 122 average time/residue: 0.2322 time to fit residues: 34.8499 Evaluate side-chains 130 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5597 Z= 0.232 Angle : 0.604 11.673 7569 Z= 0.315 Chirality : 0.044 0.203 889 Planarity : 0.004 0.060 1008 Dihedral : 6.809 58.476 802 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.83 % Allowed : 19.48 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.32), residues: 723 helix: 1.26 (0.29), residues: 310 sheet: -0.61 (0.58), residues: 92 loop : -1.73 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.018 0.001 PHE D 122 TYR 0.008 0.001 TYR D 155 ARG 0.014 0.000 ARG E 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 100 LYS cc_start: 0.7781 (tttm) cc_final: 0.7501 (tttm) REVERT: D 229 MET cc_start: 0.5725 (tpt) cc_final: 0.5447 (tpt) REVERT: D 249 GLN cc_start: 0.7721 (pp30) cc_final: 0.7207 (pp30) REVERT: D 272 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6477 (pp30) REVERT: D 283 GLN cc_start: 0.6273 (tp-100) cc_final: 0.5820 (tp-100) REVERT: D 333 LYS cc_start: 0.7442 (ttmt) cc_final: 0.7220 (ttmt) REVERT: D 356 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7535 (mm) REVERT: D 359 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6584 (mm-30) REVERT: D 382 MET cc_start: 0.6574 (ttp) cc_final: 0.6320 (ttp) REVERT: D 395 LYS cc_start: 0.7804 (tmtt) cc_final: 0.7476 (tmtt) REVERT: D 418 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: F 102 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5762 (pp) REVERT: F 117 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7448 (ttmm) REVERT: F 122 LYS cc_start: 0.8056 (tptt) cc_final: 0.7625 (tptt) outliers start: 28 outliers final: 23 residues processed: 118 average time/residue: 0.2174 time to fit residues: 31.9062 Evaluate side-chains 128 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 0.0000 chunk 41 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 476 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.194200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164088 restraints weight = 8749.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168931 restraints weight = 5289.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.172519 restraints weight = 3539.509| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5597 Z= 0.277 Angle : 0.629 11.410 7569 Z= 0.328 Chirality : 0.045 0.200 889 Planarity : 0.004 0.066 1008 Dihedral : 6.928 58.335 802 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.83 % Allowed : 20.00 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.32), residues: 723 helix: 1.19 (0.29), residues: 310 sheet: -0.67 (0.58), residues: 92 loop : -1.76 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 204 HIS 0.005 0.001 HIS D 459 PHE 0.019 0.001 PHE D 122 TYR 0.012 0.001 TYR D 155 ARG 0.016 0.000 ARG E 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.61 seconds wall clock time: 29 minutes 34.66 seconds (1774.66 seconds total)